Well, if I had my way (that is, if I were the showrunner of a live-action Batman TV show), the Joker would be the primary villain of Season 1 - not in every episode, but popping up for about 1/4 to 1/3 of the episodes. (Pilot would be the Red Hood, ending with Batman tossing him into a vat of chemicals; episode 2 or 3 would properly introduce the Joker, and he'd pop up every now and again throughout the season.) Season 1 would end with the Joker being incarcerated in Arkham.

Season 2 would see Batman visit the Joker in Arkham now and again, ostensibly for information on other villains, but really to keep tabs on his "rehabilitation." Near the end of Season 2, Harley Quinn would come into play, and help him break out of Arkham.

Season 3 and beyond would, as you say, see the Joker showing up every now and again, but not very often, and not regularly (if you want to know what I mean by "regularly," see the Daleks in post-2005 Doctor Who).

Damn it, now you've got me thinking too much about this again ... I might have to start drawing up some outlines ...

And now that I think about it, I might condense seasons 1 and 2 into a single season, so the Joker would be incarcerated at the halfway point of the season, and be broken out at the end. Possibly.